I don't know about neutralizing the soda. You are right in that it's a fairly controversial issue but it is done and frequently. I do think there are some commercial products available for this but do not know what they are off the top of my head. Google will surely reveal some answers for you.
Regarding removal of rust from the engine bay, sometimes there is no easy way to do it and my weapon of choice is a wire wheel.
After you have removed all the rust and everything is down to bare metal, you need to degrease your metal well (this is the most critical step in paint prep) with a paint prep degreasing solvent, blow and tack the metal off, and then prime all the metal with a good ETCHING primer. The etching primer is essential as it will etch into the metal which not only makes a good surface for painting, but it seals the metal too and prevents rust from coming back.
The green stuff is the Sikkens Washprimer (etching primer) I used. It's expensive ($20 a can) but it's as professional top of the line that you can get. Normally the wash primer is a two part that's mixed together when spraying but they somehow figured out how to make an aerosal one too. The haze in final picture is literally paint haze.